Set in different decades in the same house, these stories of three lesbian couples each reflect a specific concern. In 1961, Abby and Edith, two retired schoolteachers, lead a quiet life. Abby has a stroke and dies, and her nephew and his wife come for the funeral and to sort and sell Abby's things, unaware that she and Edith were a lifelong couple. In 1972, four college-age lesbians share the house. They have problems with the campus feminism group, and Linda is drawn to Amy a very butch lesbian who wears a men's clothing and drives a motorcycle. How can a feminist fall for a lesbian who acts like and dresses like a man? By 2000, long-term couple Fran and Kal want to have a child, and their quest leads from proposing sperm donation to a gay couple they know, to the horror of shopping for sperm on the Internet.

Through the works of biologist and philosopher Ernst Haeckel, the role of the sea as the "outer space" of his time is explored. Based almost entirely on 19th-century scientific illustrations, paintings, and photographs brought to life through innovative animation, Proteus explores the undersea world through a complex tapestry of biology, oceanography, scientific history, poetry and myth.